5u6b

Structure of the Axl kinase domain in complex with a macrocyclic inhibitor

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tyrosine-protein kinase receptor UFO

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;(10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3,10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno)pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one ; × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;(10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3,10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno)pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one ; × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	;(10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3,10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno)pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one ; × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	;(10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3,10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno)pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one ; × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UFO_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–307； UniProt 514–818 Author chain B； PDBConstruct 3–307； UniProt 514–818 Author chain C； PDBConstruct 3–307； UniProt 514–818 Author chain D； PDBConstruct 3–307； UniProt 514–818

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5u6b
Deposition date deposition_date	2016-12-07
Structure title title	Structure of the Axl kinase domain in complex with a macrocyclic inhibitor
Keywords keywords	Kinase Inhibitor Complex, Transferase-Transferase Inhibitor complex; Transferase/Transferase Inhibitor
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5u6b__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5u6b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5u6b__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.37 Å
Rg (electron density)	19.34 Å
Total Rg	20.26 Å
Atom count	2175
Residues	270
Excluded volume	38948 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5u6b__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5u6b__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5u6b__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5u6b__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein kinase receptor UFO
Molecular weight formula_weight	34870.0 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9046

GSNSLGISEELKEKLRDVMVDRHKVALGKTLGEGEFGAVMEGQLNQDDSILKVAVKTMKIAICTRSELEDFLSEAVCMKEFDHPNVMRLIGVCFQGSERESFPAPVVILPFMKHGDLHSFLLYSRLGDQPVYLPTQMLVKFMADIASGMEYLSTKRFIHRDLAARNCMLNENMSVCVADFGLSKKIYNGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWSFGVTMWEIATRGQTPYPGVENSEIYDYLRQGNRLKQPADCLDGLYALMSRCWELNPQDRPSFTELREDLENTLKALPPAQEPDE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	;(10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3,10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno)pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one ;
Molecular weight formula_weight	460.9 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5u6ba_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d5u6bb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d5u6bb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5u6bc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d5u6bd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d5u6bd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	5u6bA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	5u6bA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	5u6bB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	5u6bB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	5u6bC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	5u6bC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	5u6bD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	5u6bD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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Unit-cell length a length_a	81.680 Å
Unit-cell length b length_b	100.704 Å
Unit-cell length c length_c	81.921 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.840 Å
Low-resolution limit resolution_low	59.810 Å
R factor r_factor	0.2120
R_work r_work	0.2110
R_free r_free	0.2390

Structure of the Axl kinase domain in complex with a macrocyclic inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tyrosine-protein kinase receptor UFO

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5u6b__assembly_1__model_1

5u6b__assembly_1__model_1 | I(q)

5u6b__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of the Axl kinase domain in complex with a macrocyclic inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tyrosine-protein kinase receptor UFO

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5u6b__assembly_1__model_1

5u6b__assembly_1__model_1 | I(q)

5u6b__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)